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NCBI C++ ToolKit: src/gui/objutils/fasta_utils.cpp Source File

vector<CSeq_id_Handle> ids;

ids.push_back(id_hdl);

vector<CBioseq_Handle> bshs = scope.GetBioseqHandles(ids);

bsh_it = bshs.begin();

(

it =

.begin(); it !=

.end(); ++it, ++bsh_it) {

(se.

() && *bsh_it) {

(entry_len == wellknown_seqvec.

()) {

entry_seq, wellknown_seq;

entry_seqvec.

(0, entry_len, entry_seq);

wellknown_seqvec.

(0, entry_len, wellknown_seq);

(entry_seq == wellknown_seq)

list< CRef< CSeq_entry > > &seq_set = bss.

();

list< CRef< CSeq_entry > > &old_seq_set = old_bss.

();

list<ESeqStatus>

;

st_it =

.begin();

(

it = old_seq_set.begin(); it != old_seq_set.end(); ++it, ++st_it) {

(ids.size() > 1) {

= ids.begin();

ids.erase(++

, ids.end());

vector<string> parts;

(!acc.empty()) str_id = acc;

(parts.rbegin()->empty()) {

lcl_id =

+

(parts,

);

mapper.AddMapping(sih, lcl_hndl);

(

!= local_ids) {

seq_set.push_back(se);

(

!= wellknown_ids) {

wellknown_ids->push_back(sih.

());

mapper.MapObject(bss);

(local_ids.empty())

vector<CRef<CSeq_entry> >

;

entry.SetSet().SetSeq_set()) {

vector<CSeq_id_Handle> ids;

it_id = local_ids.find(id_hdl.

());

(it_id == local_ids.end())

bioseqs[it_id->second] = &seq->SetSeq();

vector<CBioseq_Handle> bshs = scope.GetBioseqHandles(ids);

(

&bsh : bshs) {

bioseq = bioseqs.

(bsh.GetSeqId());

(bioseq == bioseqs.

())

(bsh, *(bioseq->second));

(

== biosrc)

descr->

(*org_copy);

destination.

().Set().push_back(descr);

((fasta_id.find(

) == string::npos) && (fasta_id.find(

) == string::npos))

vector<string> to_replace{

,

,

};

(

&search : to_replace)

vector<string> parts;

(

&item : parts) {

(item.length() < 5)

const_iterator end() const

const_iterator find(const key_type &key) const

void CopyOrg(const CBioseq_Handle &source, CBioseq &destination)

CRef< CSeq_id > IdentifyLocalId(const string &fasta_id)

Tries to identify the specified local id (works for ids, prefixed with rng_ or mod_,...

CRef< CSeq_entry > ReplaceWellknownSeqs(CSeq_entry &entry, CScope &scope, vector< CConstRef< CSeq_id >> *wellknown_ids, TSeq_idMap *local_ids)

void GetSeqsStatus(list< CRef< CSeq_entry > > &entries, CScope &scope, list< ESeqStatus > &stat)

void UpdateOrgInformation(objects::CSeq_entry &entry, objects::CScope &scope, const TSeq_idMap &local_ids)

Updates the organism information for the Seq-entry object by copying the information from a well-know...

std::map< CConstRef< objects::CSeq_id >, CConstRef< objects::CSeq_id >, CompareSeq_ids > TSeq_idMap

Maps local ids to well-known ones.

ESeqStatus

Status of the FASTA sequence.

unsigned int TSeqPos

Type for sequence locations and lengths.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

static EAccessionInfo IdentifyAccession(const CTempString &accession, TParseFlags flags=fParse_AnyRaw)

Deduces information from a bare accession a la WHICH_db_accession; may report false negatives on prop...

CConstRef< CSeq_id > GetSeqId(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

string AsString(void) const

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

const CBioSource * GetBioSource(const CBioseq &bioseq)

Retrieve the BioSource object for a given bioseq handle.

string GetAccessionForGi(TGi gi, CScope &scope, EAccessionVersion use_version=eWithAccessionVersion, EGetIdType flags=0)

Retrieve the accession for a given GI.

@ eGetId_Best

return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

static string & Replace(const string &src, const string &search, const string &replace, string &dst, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

bool CanGetOrg(void) const

Check if it is safe to call GetOrg method.

const TOrg & GetOrg(void) const

Get the Org member data.

const TSeq & GetSeq(void) const

Get the variant data.

TSet & SetSet(void)

Select the variant.

bool CanGetAnnot(void) const

Check if it is safe to call GetAnnot method.

bool CanGetSeq_set(void) const

Check if it is safe to call GetSeq_set method.

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

bool IsSeq(void) const

Check if variant Seq is selected.

list< CRef< CSeq_entry > > TSeq_set

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

TId & SetId(void)

Assign a value to Id data member.

TOrg & SetOrg(void)

Select the variant.

const TId & GetId(void) const

Get the Id member data.

list< CRef< CSeq_id > > TId

bool CanGetId(void) const

Check if it is safe to call GetId method.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

const CharType(& source)[N]

static SLJIT_INLINE sljit_ins st(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

Compares ids as FASTA strings.

static wxAcceleratorEntry entries[3]

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